The nucleotide landscape of polyXY regions
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Pablo Mier
- Miguel A Andrade-Navarro
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:001110050600001&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1016/j.csbj.2023.10.054
- Externe Identifier
- Clarivate Analytics Document Solution ID: Z1WJ0
- PubMed Identifier: 38022702
- ISSN
- 2001-0370
- Zeitschrift
- COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
- Schlüsselwörter
- Protein sequence analysis
- Low complexity regions
- Linear motifs
- PolyXY
- Paginierung
- 5408 - 5412
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Titel
- The nucleotide landscape of polyXY regions
- Sub types
- Article
- Ausgabe der Zeitschrift
- 21
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Pablo Mier
- Miguel A Andrade-Navarro
- DOI
- 10.1016/j.csbj.2023.10.054
- ISSN
- 2001-0370
- Zeitschrift
- Computational and Structural Biotechnology Journal
- Sprache
- en
- Paginierung
- 5408 - 5412
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Herausgeber
- Elsevier BV
- Herausgeber URL
- http://dx.doi.org/10.1016/j.csbj.2023.10.054
- Datum der Datenerfassung
- 2024
- Titel
- The nucleotide landscape of polyXY regions
- Ausgabe der Zeitschrift
- 21
Datenquelle: Crossref
- Abstract
- PolyXY regions are compositionally biased regions composed of two different amino acids. They are classified according to the arrangement of the two amino acid types 'X' and 'Y' into direpeats (composed of alternating amino acids, e.g. 'XYXYXY'), joined (composed of two consecutive stretches of each amino acid, e.g. 'XXXYYY') and shuffled (other arrangements, e.g., 'XYXXYY'). They have been characterized at the amino acid level in all domains of life, and are described as often found within intrinsically disordered regions. Since DNA replication slippage has been proposed as a driver of repeat variation, and given that some polyXY have a repetitive nature, we hypothesized that characterizing the nucleotide coding of various types of polyXY could give hints about their origin and evolution. To test this, we obtained all polyXY regions in the human transcriptome, categorized them, and studied their coding nucleotide sequences. We observed that polyXY exacerbates the codon biases, and that the similarity between the X and Y codons is higher than in the background proteome. Our results support a general mechanism of emergence and evolution of polyXY from single-codon polyX. PolyXY are revealed as hotspots for replication slippage, particularly those composed of repeats: joined and direpeat polyXY. Inter-conversion to shuffled polyXY disrupts nucleotide repeats and restricts further evolution by replication slippage, a mechanism that we previously observed in polyX. Our results shed light on polyXY composition and should simplify the determination of their functions.
- Addresses
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany.
- Autoren
- Pablo Mier
- Miguel A Andrade-Navarro
- DOI
- 10.1016/j.csbj.2023.10.054
- eISSN
- 2001-0370
- Externe Identifier
- PubMed Identifier: 38022702
- PubMed Central ID: PMC10652141
- Funding acknowledgements
- European Cooperation in Science and Technology:
- Open access
- true
- ISSN
- 2001-0370
- Zeitschrift
- Computational and structural biotechnology journal
- Sprache
- eng
- Medium
- Electronic-eCollection
- Online publication date
- 2023
- Open access status
- Open Access
- Paginierung
- 5408 - 5412
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Publisher licence
- CC BY-NC-ND
- Datum der Datenerfassung
- 2023
- Titel
- The nucleotide landscape of polyXY regions.
- Sub types
- brief-report
- Journal Article
- Ausgabe der Zeitschrift
- 21
Files
http://www.csbj.org/article/S2001037023004087/pdf https://europepmc.org/articles/PMC10652141?pdf=render
Datenquelle: Europe PubMed Central
- Abstract
- PolyXY regions are compositionally biased regions composed of two different amino acids. They are classified according to the arrangement of the two amino acid types 'X' and 'Y' into direpeats (composed of alternating amino acids, e.g. 'XYXYXY'), joined (composed of two consecutive stretches of each amino acid, e.g. 'XXXYYY') and shuffled (other arrangements, e.g., 'XYXXYY'). They have been characterized at the amino acid level in all domains of life, and are described as often found within intrinsically disordered regions. Since DNA replication slippage has been proposed as a driver of repeat variation, and given that some polyXY have a repetitive nature, we hypothesized that characterizing the nucleotide coding of various types of polyXY could give hints about their origin and evolution. To test this, we obtained all polyXY regions in the human transcriptome, categorized them, and studied their coding nucleotide sequences. We observed that polyXY exacerbates the codon biases, and that the similarity between the X and Y codons is higher than in the background proteome. Our results support a general mechanism of emergence and evolution of polyXY from single-codon polyX. PolyXY are revealed as hotspots for replication slippage, particularly those composed of repeats: joined and direpeat polyXY. Inter-conversion to shuffled polyXY disrupts nucleotide repeats and restricts further evolution by replication slippage, a mechanism that we previously observed in polyX. Our results shed light on polyXY composition and should simplify the determination of their functions.
- Date of acceptance
- 2023
- Autoren
- Pablo Mier
- Miguel A Andrade-Navarro
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/38022702
- DOI
- 10.1016/j.csbj.2023.10.054
- Externe Identifier
- PubMed Central ID: PMC10652141
- ISSN
- 2001-0370
- Zeitschrift
- Comput Struct Biotechnol J
- Schlüsselwörter
- Linear motifs
- Low complexity regions
- PolyXY
- Protein sequence analysis
- Sprache
- eng
- Country
- Netherlands
- Paginierung
- 5408 - 5412
- PII
- S2001-0370(23)00408-7
- Datum der Veröffentlichung
- 2023
- Status
- Published online
- Titel
- The nucleotide landscape of polyXY regions.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 21
Datenquelle: PubMed
- Beziehungen:
- Eigentum von